Available Methods
Bio::EnsEMBL::LookUp::LocalLookUp Class Reference

List of all members.

Class Summary

Synopsis

# creation from a database server
Bio::EnsEMBL::LookUp::LocalLookUp->register_all_dbs( $conf->{host},
       $conf->{port}, $conf->{user}, $conf->{pass}, $conf->{db});
my $lookup = Bio::EnsEMBL::LookUp::LocalLookUp->new();
my $dbas = $lookup->registry()->get_all();
$dbas = $lookup->get_all_by_taxon_id(388919);
$dbas = $lookup->get_by_name_pattern("Escherichia.*");

# creation from a URL
my $lookup = Bio::EnsEMBL::LookUp::::LocalLookUp->new(-URL=>'http://bacteria.ensembl.org/registry.json');

Description

This module is an implementation of Bio::EnsEMBL::LookUp that uses a local hash to store information about available Ensembl Genomes data. 
It can be constructed in a number of different ways:

A remote cache file containing a JSON representation of the hash can be supplied:

	my $lookup = Bio::EnsEMBL::LookUp::LocalLookUp->new(-URL=>'http://bacteria.ensembl.org/registry.json');

Alternatively, a local file containing the required JSON can be specified instead:

	my $lookup = Bio::EnsEMBL::LookUp::LocalLookUp->new(-FILE=>"/path/to/reg.json");

Finally, a Registry already loaded with core databases can be supplied:

	my $lookup = Bio::EnsEMBL::LookUp::LocalLookUp->new(-REGISTRY=>'Bio::EnsEMBL::Registry');

If the standard Registry is used, the Arg can be omitted completely:

	my $lookup = Bio::EnsEMBL::LookUp::LocalLookUp->new();

To populate the registry with just the Ensembl Genomes databases for the current software 
release on a specified server, the following method can be used:

	Bio::EnsEMBL::LookUp::LocalLookUp->register_all_dbs( $host,
	   $port, $user, $pass);

Once a lookup has been created, it can be used as specified in Bio::EnsEMBL::LookUp

See-also

Bio::EnsEMBL::LookUp

Definition at line 66 of file LocalLookUp.pm.

Available Methods

protected _add_aliases ()
protected _check_name ()
protected _dba_id ()
protected _dba_to_locator ()
protected _dbc_to_locator ()
protected _get_dbc_meta ()
protected _hash_dba ()
protected _hash_dba_from_values ()
protected _intern_db_connections ()
protected _invert_dba_hash ()
protected _load_registry_from_json ()
protected _login_hash ()
protected _query_multispecies_db ()
protected void _register_dba ()
protected _register_multispecies_core ()
protected _register_multispecies_x ()
protected _register_singlespecies_core ()
protected Arrayref _registry_to_hash ()
protected _registry_to_json ()
protected _runtime_include ()
public File cache_file ()
public clear_cache ()
public Arrayref dba_to_args ()
public Arrayref get_all ()
public Arrayref get_all_accessions ()
public Arrayref get_all_assemblies ()
public Arrayref get_all_by_accession ()
public Arrayref get_all_by_dbname ()
public Arrayref get_all_by_name_pattern ()
public get_all_by_taxon_branch ()
public Arrayref get_all_by_taxon_id ()
public Arrayref get_all_DBConnections ()
public Arrayref get_all_dbnames ()
public Arrayref get_all_names ()
public Arrayref get_all_taxon_ids ()
public Arrayref get_all_versioned_accessions ()
public Arrayref get_all_versioned_assemblies ()
public
Bio::EnsEMBL::DBSQL::DatabaseAdaptor 		get_by_assembly_accession ()
public Arrayref get_by_name_exact ()
public load_registry_from_file ()
public load_registry_from_url ()
public new ()
public void register_all_dbs ()
public Registry registry ()
public
Bio::EnsEMBL::Taxonomy::DBSQL::DBAdaptor 		taxonomy_adaptor ()
public update_from_registry ()
public void write_registry_to_file ()

Method Documentation

protected Bio::EnsEMBL::LookUp::LocalLookUp::_add_aliases ( ) 
	Description : Registry all aliases
	Arg	: Species name
	Arg	: Arrayref of alias strings
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protected Bio::EnsEMBL::LookUp::LocalLookUp::_check_name ( ) 
	Description : Check that the name is not longer than 64 characters
	Arg	: Name to check
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protected Bio::EnsEMBL::LookUp::LocalLookUp::_dba_id ( )

Undocumented method

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protected Bio::EnsEMBL::LookUp::LocalLookUp::_dba_to_locator ( ) 
	Description : return a hash key for a DBAdaptor
	Arg	: Bio::EnsEMBL::DBAdaptor
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protected Bio::EnsEMBL::LookUp::LocalLookUp::_dbc_to_locator ( ) 
	Description : return a hash key for a DBConnection
	Arg	: Bio::EnsEMBL::DBConnection
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protected Bio::EnsEMBL::LookUp::LocalLookUp::_get_dbc_meta ( )

Undocumented method

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protected Bio::EnsEMBL::LookUp::LocalLookUp::_hash_dba ( ) 
	Description : Add details from a DBAdaptor to the internal hashes of details
	Arg	: Bio::EnsEMBL::DBAdaptor
	Arg 	: (optional) If set to 1, do not update from a DBAdaptor if already processed (allows updates of an existing LookUp instance)
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protected Bio::EnsEMBL::LookUp::LocalLookUp::_hash_dba_from_values ( ) 
	Description : Add supplied details to the internal hashes of details
	Arg	: Bio::EnsEMBL::DBAdaptor to hash
	Arg	: Arrayref of taxonomy IDs to use as keys
	Arg	: Arrayref of aliases to use as keys
	Arg	: Arrayref of ENA accessions to use as keys
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protected Bio::EnsEMBL::LookUp::LocalLookUp::_intern_db_connections ( ) 
  Description : Go through all available DBAdaptors of registry and ensure they use the same
                DBConnection instance.
  Exceptions  : None
  Status      : At Risk
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protected Bio::EnsEMBL::LookUp::LocalLookUp::_invert_dba_hash ( )

Undocumented method

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protected Bio::EnsEMBL::LookUp::LocalLookUp::_load_registry_from_json ( ) 
	Description	: load the registry from the supplied JSON string
	Arg	: JSON string
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protected Bio::EnsEMBL::LookUp::LocalLookUp::_login_hash ( ) 
	Description : Generate dbadaptor login hash from supplied Args
	Arg	: Host
	Arg	: Port
	Arg	: User
	Arg	: Password
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protected Bio::EnsEMBL::LookUp::LocalLookUp::_query_multispecies_db ( ) 
	Description : Find all species in the multispecies database
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protected void Bio::EnsEMBL::LookUp::LocalLookUp::_register_dba ( ) 
	Description	: Add a single DBAdaptor to the registry and the internal hashes of details
	Arg	: Bio::EnsEMBL::DBSQL::DBAdaptor
	Return		: None
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protected Bio::EnsEMBL::LookUp::LocalLookUp::_register_multispecies_core ( ) 
	Description : Register core dbas for all species in the supplied database
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protected Bio::EnsEMBL::LookUp::LocalLookUp::_register_multispecies_x ( ) 
	Description : Register specified dba type for all species in the supplied database
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protected Bio::EnsEMBL::LookUp::LocalLookUp::_register_singlespecies_core ( ) 
	Description : Register core dbas for all species in the supplied database
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protected Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::_registry_to_hash ( ) 
	Description	: Generate a hash array structure for the current registry and species details for turning to JSON
	Returns		: Arrayref of hashes
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protected Bio::EnsEMBL::LookUp::LocalLookUp::_registry_to_json ( )

Undocumented method

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protected Bio::EnsEMBL::LookUp::LocalLookUp::_runtime_include ( ) 
	Description : Load the specified module (usually a DatabaseAdaptor)
	Arg 	: Module name
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public File Bio::EnsEMBL::LookUp::LocalLookUp::cache_file ( ) 
  Arg [1]     : File to use for local caching
  Description : Sets and retrieves the local cache file 
  Returntype  : File name if set; otherwise undef
  Status      : Stable
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public Bio::EnsEMBL::LookUp::LocalLookUp::clear_cache ( )

Undocumented method

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public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::dba_to_args ( ) 
	Description	: Dump the Args needed for contructing a DBA
	Arg	: Bio::EnsEMBL::DBAdaptor
	Return		: Arrayref of args
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public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_all ( ) 
	Description : Return all database adaptors that have been retrieved from registry
	Arg    : None
	Exceptions  : None
	Return type : Arrayref of Bio::EnsEMBL::DBSQL::DatabaseAdaptor
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public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_all_accessions ( ) 
	Description : Return list of all INSDC sequence accessions (or other seq_region names) registered with the helper
	Exceptions  : None
	Return type : Arrayref of strings
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public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_all_assemblies ( ) 
	Description : Return list of all INSDC assembly accessions registered with the helper
	Exceptions  : None
	Return type : Arrayref of strings
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public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_all_by_accession ( ) 
	Description : Returns the database adaptor(s) that contains a seq_region with the supplied INSDC accession (or other seq_region name)
	Arg    : Int
	Exceptions  : None
	Return type : Arrayref of Bio::EnsEMBL::DBSQL::DatabaseAdaptor
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public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_all_by_dbname ( ) 
	Description : Returns all database adaptors that have the supplied dbname
	Arg    : String
	Exceptions  : None
	Return type : Arrayref of Bio::EnsEMBL::DBSQL::DatabaseAdaptor
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public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_all_by_name_pattern ( ) 
	Description : Return all database adaptors that have an alias/name that match the supplied regexp
	Arg    : String
	Exceptions  : None
	Return type : Arrayref of Bio::EnsEMBL::DBSQL::DatabaseAdaptor
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public Bio::EnsEMBL::LookUp::LocalLookUp::get_all_by_taxon_branch ( )

Undocumented method

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public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_all_by_taxon_id ( ) 
	Description : Returns all database adaptors that have the supplied taxonomy ID
	Arg    : Int
	Exceptions  : None
	Return type : Arrayref of Bio::EnsEMBL::DBSQL::DatabaseAdaptor
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public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_all_DBConnections ( ) 
	Description : Return all database connections used by the DBAs retrieved from the registry
	Arg    : None
	Exceptions  : None
	Return type : Arrayref of Bio::EnsEMBL::DBSQL::DBConnection
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public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_all_dbnames ( ) 
	Description : Return all database names used by the DBAs retrieved from the registry
	Arg    : None
	Exceptions  : None
	Return type : Arrayref of strings
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public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_all_names ( ) 
	Description : Return list of all species names registered with the helper
	Exceptions  : None
	Return type : Arrayref of strings
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public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_all_taxon_ids ( ) 
	Description : Return list of all taxon IDs registered with the helper
	Exceptions  : None
	Return type : Arrayref of integers
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public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_all_versioned_accessions ( ) 
	Description : Return list of all versioned INSDC sequence accessions (or other seq_region names) registered with the helper
	Exceptions  : None
	Return type : Arrayref of strings
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public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_all_versioned_assemblies ( ) 
	Description : Return list of all versioned INSDC assembly accessions registered with the helper
	Exceptions  : None
	Return type : Arrayref of strings
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public Bio::EnsEMBL::DBSQL::DatabaseAdaptor Bio::EnsEMBL::LookUp::LocalLookUp::get_by_assembly_accession ( ) 
	Description : Returns the database adaptor that contains the assembly with the supplied INSDC assembly accession
	Arg    : Int
	Exceptions  : None
	Return type : Bio::EnsEMBL::DBSQL::DatabaseAdaptor
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public Arrayref Bio::EnsEMBL::LookUp::LocalLookUp::get_by_name_exact ( ) 
	Description : Return all database adaptors that have the supplied string as an alias/name
	Arg    : String
	Exceptions  : None
	Return type : Arrayref of Bio::EnsEMBL::DBSQL::DatabaseAdaptor
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public Bio::EnsEMBL::LookUp::LocalLookUp::load_registry_from_file ( )

Undocumented method

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public Bio::EnsEMBL::LookUp::LocalLookUp::load_registry_from_url ( )

Undocumented method

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public Bio::EnsEMBL::LookUp::LocalLookUp::new ( )

Undocumented method

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public void Bio::EnsEMBL::LookUp::LocalLookUp::register_all_dbs ( ) 
	Description : Helper method to load the registry with all multispecies core databases on the supplied server
	Arg    : Host
	Arg    : Port
	Arg    : User
	Arg    : Password
	Arg    : (optional) String with database regexp (default is _collection_core_[0-9]_eVersion_[0-9]+)
	Exceptions  : None
	Return type : None
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public Registry Bio::EnsEMBL::LookUp::LocalLookUp::registry ( ) 
  Arg [1]     : Registry module to use (default is Bio::EnsEMBL::Registry)
  Description : Sets and retrieves the Registry 
  Returntype  : Registry if set; otherwise undef
  Exceptions  : if an attempt is made to set the value more than once
  Status      : Stable
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public Bio::EnsEMBL::Taxonomy::DBSQL::DBAdaptor Bio::EnsEMBL::LookUp::LocalLookUp::taxonomy_adaptor ( ) 
	Description	: Get/set the taxonomy adaptor
	Arg	: (optional) Bio::EnsEMBL::Taxonomy::DBSQL::DBAdaptor
	Caller    : Internal
	Status    : Stable
	Return		: Bio::EnsEMBL::Taxonomy::DBSQL::DBAdaptor
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public Bio::EnsEMBL::LookUp::LocalLookUp::update_from_registry ( ) 
	Description : Update internal hashes of database adaptors by name/taxids from the registry. Invoke when registry has been updated independently.
	Arg 	: (optional) If set to 1, do not update from a DBAdaptor if already processed (allows updates of an existing LookUp instance)
	Exceptions  : None
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public void Bio::EnsEMBL::LookUp::LocalLookUp::write_registry_to_file ( ) 
	Description	: Write the contents of the registry and species lists to a JSON file
	Arg	: File name
	Return		: None
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The documentation for this class was generated from the following file: